8E1G | pdb_00008e1g

SARS-CoV-2 RBD in complex with Omicron-neutralizing antibody 2A10

• PDB DOI: https://doi.org/10.2210/pdb8E1G/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Homo sapiens, Severe acute respiratory syndrome coronavirus 2
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2022-08-10 Released: 2023-06-28 
• Deposition Author(s): Wasserman, H., Hastie, K.M., Buck, T.K., Saphire, E.O.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Potent Omicron-neutralizing antibodies isolated from a patient vaccinated 6 months before Omicron emergence.

Hastie, K.M., Yu, X., Ana-Sosa-Batiz, F., Zyla, D.S., Harkins, S.S., Hariharan, C., Wasserman, H., Zandonatti, M.A., Miller, R., Maule, E., Kim, K., Valentine, K.M., Shresta, S., Saphire, E.O.

(2023) Cell Rep 42: 112421-112421

• PubMed: 37083327 
• DOI: https://doi.org/10.1016/j.celrep.2023.112421
• Primary Citation Related Structures: 
  8E1G, 8F0G, 8F0H


• PubMed Abstract: 
  

  Therapeutic antibodies are an important tool in the arsenal against coronavirus infection. However, most antibodies developed early in the pandemic have lost most or all efficacy against newly emergent strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), particularly those of the Omicron lineage. Here, we report the identification of a panel of vaccinee-derived antibodies that have broad-spectrum neutralization activity. Structural and biochemical characterization of the three broadest-spectrum antibodies reveal complementary footprints and differing requirements for avidity to overcome variant-associated mutations in their binding footprints. In the K18 mouse model of infection, these three antibodies exhibit protective efficacy against BA.1 and BA.2 infection. This study highlights the resilience and vulnerabilities of SARS-CoV-2 antibodies and provides road maps for further development of broad-spectrum therapeutics.

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Organizational Affiliation: 
• Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA. Electronic address: [e-mail].
Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92038, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 158.34 kDa 
• Atom Count: 10,185 
• Modeled Residue Count: 1,314 
• Deposited Residue Count: 1,438 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2A10 Fab, heavy chain	A [auth H], B [auth V]	224	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
2A10 Fab, light chain	C [auth L], D [auth T]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	E [auth A], F [auth B]	281	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P0DTC2-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.896	α = 90
b = 117.944	β = 90
c = 150.311	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
autoPROC	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Wasserman, H., Hastie, K.M., Buck, T.K., Saphire, E.O.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary